The experiment aimed at determining the efficient use of phytase (Phy) in Atlantic salmon diets that had low (4.5%) fishmeal and contained 60% soy protein concentrate (SPC). Phytase was either included at 250, 500, 1,000 or 4,000 U Phy kg−1 diet or the SPC was pre-treated prior to making diets using 250, 500 or 1,000 U Phy kg−1 SPC. Fish were fed the experimental diets for 12 weeks, and there were no differences in survival among treatments nor were there differences in growth performance between the phytase-pre-treated SPC diets. Feed intake and weight gain were significantly lower for diets supplemented below 1,000 U Phy kg−1 compared to all other diets. Apparent digestibility (AD) of phosphorus was significantly lower without the use of phytase (45.43 ± 2.06%) than for all other treatments. AD phosphorus increased from 55.70 ± 1.81% at the lowest phytase supplementation (250 U Phy kg−1) to 80.87 ± 2.12% at the highest (4,000 U Phy kg−1). There was no difference in AD phosphorus between the diet with the highest supplementation (4,000 U Phy kg−1) and the pre-treated diets. There were no differences in whole-body dry material, crude protein or total lipid, whereas bone ash was significantly lower for diets supplemented below 1,000 U Phy kg−1. Ash and phosphorus in the whole body and bone increased with increasing added phytase. At and above an inclusion of 1,000 U Phy kg−1, bone ash (51.26 ± 0.12% bone weight) and bone phosphorus (11.21 ± 0.04% bone weight) reached concentrations that were no different to the pre-treated diets. In conclusion, phytase improved Atlantic salmon’s growth performance fed low fishmeal diets containing SPC, and at least 1,000 U Phy kg−1 diet was required to have the same effect as pre-treatment of SPC with 250 U Phy kg−1 SPC.